Preprocessing

Motif search

Others

The Fit3D webserver implements the JavaScript-based Protein
Viewer from Marco Biasini .
The zoom level can be controlled with the mouse wheel. You can
manipulate the point of view by pressing the middle mouse button
or by holding down the Shift-key. To center the point of view
double click with the left mouse button.

One against one alignment for a single match found by
Fit3D. The green ball-stick structure represents the query
motif. Residues of the query motif are labeled in green, whereas
the corresponding match is labeled in black on gray background.

One against all alignment for the query motif against all
matches found by Fit3D. The residues of the query motif are
labeled in green.

Global alignment of the query motif source structure
(green) with a structure where a match occurred (grey). The
superimposition is based on the matching residues of the
query and the target structure. Hence, non-homologous structures
can be easily recognized to verify whether a match occurred due
to global structural similarity or convergent evolution.

Meta information

Additionally, the toolbox shows information about the query
structure when needed (submit a job or extract a motif).
Additionally, target lists uploaded by the user are analyzed. When
the calculation is finished, some statistics of the results are
presented (e.g. intra-/inter-molecular occurrences,
maximal/minimal RMSD values). Furthermore, the user can
recapitulate the original parameters of the job when inspecting
the results.

The theory behind the Fit3D algorithm
was recently published in Journal of Computational Biology.
Check out the paper to learn how our method works and to see how it
performs in contrast to existing approaches.